Merge pull request #28 from kmnhan/dev-2.4

2.4 Release

docs/environment.yml

@@ -32,7 +32,6 @@ dependencies:
   - nbsphinx
   - furo
   - sphinx-design
-  - pyperclip
   - ipywidgets
   - pip:
     - pyqt6>=6.2.2

docs/requirements.txt

@@ -1,36 +1,4 @@
 dask>=2024.4.1
-h5netcdf>=1.2.0
-igor2>=0.5.6
-iminuit>=2.25.2
-joblib>=1.3.2
-lmfit>=1.2.0,!=1.3.0
-matplotlib>=3.8.0
-numba>=0.59.0
-numbagg>=0.8.1
-numpy>=1.26.0
-pyperclip>=1.8.2
 pyqt6>=6.2.2
-PyQt6-Qt6<6.7.0
-pyqtgraph>=0.13.1
-qtawesome>=1.3.1
-qtpy>=2.4.1
-scipy>=1.12.0
-tqdm>=4.66.2
-uncertainties>=3.1.4
-varname>=0.13.0
-xarray>=2024.02.0
-sphinx
-sphinx-autodoc-typehints
-setuptools
-nbsphinx
-furo
-sphinx-design
-sphinx-qt-documentation
-sphinx-copybutton
-sphinxcontrib-bibtex
-pybtex
-hvplot
-csaps
 ipykernel
-ipywidgets
--e .
+-e '.[viz,perf,misc,docs]'

docs/source/conf.py

@@ -71,9 +71,7 @@
 
 # based on numpy doc/source/conf.py
 def linkcode_resolve(domain, info):
-    """
-    Determine the URL corresponding to Python object
-    """
+    """Determine the URL corresponding to Python object."""
     if domain != "py":
         return None
 
@@ -123,23 +121,20 @@ def linkcode_resolve(domain, info):
 autosummary_generate = True
 autosummary_generate_overwrite = True
 
-autodoc_inherit_docstrings = False
-autodoc_typehints = "description"
-autodoc_typehints_format = "short"
 autodoc_class_signature = "mixed"
-autodoc_member_order = "bysource"
+autodoc_member_order = "groupwise"
 autodoc_default_options = {
     "members": True,
     "undoc-members": True,
-    # "exclude-members":("sigDataChanged",),
     "show-inheritance": False,
 }
+autodoc_typehints = "description"
 autodoc_typehints_description_target = "documented"
+# autodoc_type_aliases = {}
+autodoc_typehints_format = "short"
+autodoc_preserve_defaults = True
+autodoc_inherit_docstrings = False
 
-# autodoc_type_aliases = {
-# "numpy.float64": "float",
-# "float64": "float",
-# }
 
 # -- Napoleon settings -------------------------------------------------------
 
@@ -149,17 +144,26 @@ def linkcode_resolve(domain, info):
 # napoleon_include_private_with_doc = False
 napoleon_include_special_with_doc = True
 # napoleon_use_admonition_for_examples = False
-# napoleon_use_admonition_for_notes = False
+napoleon_use_admonition_for_notes = True
 # napoleon_use_admonition_for_references = False
-# napoleon_use_ivar = False
+napoleon_use_ivar = True
 napoleon_use_param = True
+napoleon_use_keyword = False
 # napoleon_use_rtype = True
 napoleon_preprocess_types = True
-# napoleon_type_aliases = {
-#     "array-like": "ndarray <numpy.ndarray>",
-#     "numpy.float64": "float",
-#     "float64": "float",
-# }
+
+napoleon_type_aliases = {
+    "np.float32": "float32",
+    "numpy.float32": "float32",
+    "np.float64": "float64",
+    "numpy.float64": "float64",
+    "xr.DataArray": "xarray.DataArray",
+    "array-like": "`array-like <numpy.typing.ArrayLike>`",
+    "array_like": "`array-like <numpy.typing.ArrayLike>`",
+    "ColorType": "`ColorType <matplotlib.typing.ColorType>`",
+    "RGBColorType": "`RGBColorType <matplotlib.typing.RGBColorType>`",
+    "RGBAColorType": "`RGBAColorType <matplotlib.typing.RGBAColorType>`",
+}
 napoleon_attr_annotations = True
 napoleon_custom_sections = [("Signals", "params_style")]
 
@@ -214,8 +218,9 @@ def top_level(children, data):
 
 
 class APSStyle(pybtex.style.formatting.unsrt.Style):
-    """
-    APS style for BibTeX formatting, adapted from the conf.py file of the `mitiq
+    """APS style for BibTeX formatting.
+
+    Adapted from the conf.py file of the `mitiq
     library<https://github.com/unitaryfund/mitiq>`_.
     """
 
@@ -465,14 +470,14 @@ def get_inproceedings_template(self, e):
             "class": "",
         },
     ],
-    "light_css_variables": {
-        "color-brand-primary": "#6d50bf",
-        "color-brand-content": "#6d50bf",
-    },
-    "dark_css_variables": {
-        "color-brand-primary": "#a180ff",
-        "color-brand-content": "#a180ff",
-    },
+    # "light_css_variables": {
+    #     "color-brand-primary": "#6d50bf",
+    #     "color-brand-content": "#6d50bf",
+    # },
+    # "dark_css_variables": {
+    #     "color-brand-primary": "#a180ff",
+    #     "color-brand-content": "#a180ff",
+    # },
 }
 
 # -- LaTeX options -----------------------------------------------------------

docs/source/contributing.rst

@@ -138,7 +138,7 @@ reflected in the package without having to reinstall it. Before installing:
 
    .. code-block:: sh
 
-     pip install -e . --config-settings editable_mode=compat
+     pip install -e ".[dev]" --config-settings editable_mode=compat
 
 
 Updating the editable installation

docs/source/getting-started.rst

@@ -11,6 +11,8 @@ conda environment, you can install ERLabPy with the conda command line tool: ::
 
   conda install -c conda-forge erlab
 
+Add any `optional dependencies`_ you want to install to the command above.
+
 .. hint::
 
   If you are using macOS, you might experience degraded performance with the
@@ -31,7 +33,14 @@ conda environment, you can install ERLabPy with the conda command line tool: ::
 
 If you don’t use conda, you can install ERLabPy with pip: ::
 
-  pip install erlab
+  python -m pip install erlab
+
+Optional dependency groups can be installed with the following commands: ::
+
+  python -m pip install erlab[viz]       # Install optional dependencies for visualization
+  python -m pip install erlab[perf]      # Install optional dependencies for performance
+  python -m pip install erlab[misc]      # Install miscellaneous optional dependencies
+  python -m pip install erlab[complete]  # Install all optional dependencies
 
 If you wish to install ERLabPy from source, see the :doc:`contributing`.
 
@@ -70,26 +79,14 @@ select the appropriate library based on what is installed.
 
 See the :doc:`user-guide/index` to start using ERLabPy!
 
-Notes on compatibility
-----------------------
-
-- ERLabPy is tested on Python 3.11 and 3.12. It is not guaranteed to work on older
-  versions of Python.
-- There are some `known compatibility issues
-  <https://github.com/kmnhan/erlabpy/issues/17>`_ with PyQt5 and PySide2, so it is
-  recommended to use the newer PyQt6 or PySide6 if possible.
-- If you meet any unexpected behaviour while using IPython's `autoreload extension
-  <https://ipython.readthedocs.io/en/stable/config/extensions/autoreload.html>`_, try
-  excluding the following modules: ::
-
-    %aimport -erlab.io.dataloader -erlab.accessors
+.. _optional dependencies:
 
 Optional dependencies
 ---------------------
 
-The following packages are optional dependencies that are not installed by
-default. They are used in only specific functions, or is not used at all but is
-listed just for convenience.
+The following packages are optional dependencies that are not installed by default. They
+are only used in specific functions, or is not used at all but is listed just for
+convenience.
 
 .. list-table::
     :header-rows: 1
@@ -100,18 +97,39 @@ listed just for convenience.
       - Description
     * - `csaps <https://github.com/espdev/csaps>`_
       - Multidimensional smoothing splines
+    * - `ipywidgets <https://github.com/jupyter-widgets/ipywidgets>`_
+      - Interactive widgets
     * - `hvplot <https://github.com/holoviz/hvplot>`_ and `bokeh
         <https://github.com/bokeh/bokeh>`_
       - Interactive plotting
     * - `cmasher <https://cmasher.readthedocs.io>`_,
         `cmocean <https://matplotlib.org/cmocean/>`_, and
         `colorcet <https://colorcet.holoviz.org>`_
       - More colormaps!
+    * - `numbagg <https://github.com/numbagg/numbagg>`_ and `bottleneck
+        <https://github.com/pydata/bottleneck>`_
+      - Fast multidimensional aggregation, accelerates xarray
 
-For a full list of dependencies and optional dependencies, take a look at the ``[project]`` and ``[project.optional-dependencies]`` section in
-`pyproject.toml <https://github.com/kmnhan/erlabpy/blob/main/pyproject.toml>`_:
+For a full list of dependencies and optional dependencies, take a look at the
+``[project]`` and ``[project.optional-dependencies]`` section in `pyproject.toml
+<https://github.com/kmnhan/erlabpy/blob/main/pyproject.toml>`_:
 
 .. literalinclude:: ../../pyproject.toml
    :language: toml
    :start-at: dependencies = [
    :end-before: [project.urls]
+
+
+Notes on compatibility
+----------------------
+
+- ERLabPy is tested on Python 3.11 and 3.12. It is not guaranteed to work on older
+  versions of Python.
+- There are some `known compatibility issues
+  <https://github.com/kmnhan/erlabpy/issues/17>`_ with PyQt5 and PySide2, so it is
+  recommended to use the newer PyQt6 or PySide6 if possible.
+- If you meet any unexpected behaviour while using IPython's `autoreload extension
+  <https://ipython.readthedocs.io/en/stable/config/extensions/autoreload.html>`_, try
+  excluding the following modules: ::
+
+    %aimport -erlab.io.dataloader -erlab.accessors

docs/source/user-guide/curve-fitting.ipynb

@@ -45,7 +45,6 @@
                 "import matplotlib.pyplot as plt\n",
                 "import numpy as np\n",
                 "import xarray as xr\n",
-                "\n",
                 "from erlab.io.exampledata import generate_data"
             ]
         },
@@ -423,7 +422,7 @@
                 "model = MultiPeakModel(npeaks=4, peak_shapes=[\"lorentzian\"], fd=False, convolve=True)\n",
                 "\n",
                 "params = model.make_params(\n",
-                "    p0_center=-0.59,\n",
+                "    p0_center=-0.6,\n",
                 "    p1_center=-0.45,\n",
                 "    p2_center=0.45,\n",
                 "    p3_center=0.6,\n",
@@ -995,7 +994,7 @@
                 "    model,\n",
                 "    mdc,\n",
                 "    mdc.kx,\n",
-                "    p0_center=-0.59,\n",
+                "    p0_center=-0.6,\n",
                 "    p1_center=-0.45,\n",
                 "    p2_center=0.45,\n",
                 "    p3_center=0.6,\n",